Literature DB >> 11511264

On the magnitude and specificity of medium effects in enzyme-like catalysts for proton transfer.

F Hollfelder1, A J Kirby, D S Tawfik.   

Abstract

Medium effects are normally studied by comparing the rates of reactions in different solvents. However, medium effects at the active site of enzymes differ dramatically from bulk solvents, both in their diversity (the presence of more than one type of "solvent") and in their spatial arrangement. We describe medium effects in a simple catalytic system, obtained by systematic alkylation of a polymeric scaffold bearing amine groups to give synzymes that catalyze the Kemp elimination of benzisoxazoles with remarkable efficiency. Our analysis indicates that catalysis by these synzymes is driven primarily by specific, localized enzyme-like medium effects, and these effects seem to differ dramatically from the nonspecific medium effects (i.e., desolvation activation) exhibited by solvents. Ligand-binding studies indicate that the synzyme active sites provide localized microenvironments affording a combination of hydrophobic and apolar regions on one hand and dipolar, protic, and positively charged on the other. Such localized microenvironments are not available in bulk solvents. A Brønsted (leaving group) analysis indicates that, in comparison to solvent catalysis, the efficiency of synzyme catalysis shows little sensitivity to leaving group pK(a). We show that enzyme-like medium effects alone, in the absence of efficient positioning of the catalytic amine base relative to the substrate, can give rise to rate accelerations as high as 10(5), for both activated and nonactivated substrates. Supported by the accidental identification of active sites on the surfaces of noncatalytic proteins and the promiscuous activities found in many enzymes, our findings suggest that the interfaces of protein surfaces and their hydrophobic cores provide a microenvironment that is intrinsically active and may serve as a basis for further evolutionary improvements to give proficient and selective enzymes.

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Year:  2001        PMID: 11511264     DOI: 10.1021/jo015723v

Source DB:  PubMed          Journal:  J Org Chem        ISSN: 0022-3263            Impact factor:   4.354


  12 in total

1.  Catalytic and binding poly-reactivities shared by two unrelated proteins: The potential role of promiscuity in enzyme evolution.

Authors:  L C James; D S Tawfik
Journal:  Protein Sci       Date:  2001-12       Impact factor: 6.725

2.  Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution.

Authors:  Olga Khersonsky; Daniela Röthlisberger; Andrew M Wollacott; Paul Murphy; Orly Dym; Shira Albeck; Gert Kiss; K N Houk; David Baker; Dan S Tawfik
Journal:  J Mol Biol       Date:  2011-01-28       Impact factor: 5.469

3.  Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59.

Authors:  Olga Khersonsky; Gert Kiss; Daniela Röthlisberger; Orly Dym; Shira Albeck; Kendall N Houk; David Baker; Dan S Tawfik
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-08       Impact factor: 11.205

4.  Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase.

Authors:  Maria P Frushicheva; Jie Cao; Zhen T Chu; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-09       Impact factor: 11.205

5.  Kemp Eliminase Activity of Ketosteroid Isomerase.

Authors:  Vandana Lamba; Enis Sanchez; Lauren Rose Fanning; Kathryn Howe; Maria Alejandra Alvarez; Daniel Herschlag; Marcello Forconi
Journal:  Biochemistry       Date:  2017-01-20       Impact factor: 3.162

6.  Kemp Elimination in Cationic Micelles: Designed Enzyme-Like Rates Achieved through the Addition of Long-Chain Bases.

Authors:  Enis Sanchez; Steven Lu; Carson Reed; Joshua Schmidt; Marcello Forconi
Journal:  J Phys Org Chem       Date:  2015-12-01       Impact factor: 2.391

7.  Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis.

Authors:  Maria P Frushicheva; Jie Cao; Arieh Warshel
Journal:  Biochemistry       Date:  2011-04-15       Impact factor: 3.162

8.  Highly efficient catalysis of the Kemp elimination in the cavity of a cubic coordination cage.

Authors:  William Cullen; M Cristina Misuraca; Christopher A Hunter; Nicholas H Williams; Michael D Ward
Journal:  Nat Chem       Date:  2016-02-15       Impact factor: 24.427

9.  Structural origins of efficient proton abstraction from carbon by a catalytic antibody.

Authors:  Erik W Debler; Shuichiro Ito; Florian P Seebeck; Andreas Heine; Donald Hilvert; Ian A Wilson
Journal:  Proc Natl Acad Sci U S A       Date:  2005-03-23       Impact factor: 11.205

10.  High rates and substrate selectivities in water by polyvinylimidazoles as transaminase enzyme mimics with hydrophobically bound pyridoxamine derivatives as coenzyme mimics.

Authors:  Rachid Skouta; Sujun Wei; Ronald Breslow
Journal:  J Am Chem Soc       Date:  2009-11-04       Impact factor: 15.419

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